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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:23:16 +0000
parents 88d7ed7fd423
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a9a33311afc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
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1 <tool id="samtools_slice_bam" name="Slice" version="2.0.3" profile="@PROFILE@">
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2 <description>BAM by genomic regions</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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11 <command><![CDATA[
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12 ln -s '${input_bam}' temp_input.bam &&
22a1a2406fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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13 ln -s '${input_bam.metadata.bam_index}' temp_input.bam.bai &&
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15 #if str($slice_method.slice_method_selector) == "bed":
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16 samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam &&
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17 #elif str($slice_method.slice_method_selector) == "chr":
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18 samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
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19 ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } &&
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20 #elif str($slice_method.slice_method_selector) == "man":
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21 samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
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22
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23 #for $region in $slice_method.regions:
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24 "${region.chrom}:${region.start}-${region.end}"
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25 #end for
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26 &&
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27 #end if
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28
4
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29 samtools sort
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30 -O bam
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bfeeedad5354 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
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31 -T "\${TMPDIR:-.}"
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32 -@ \${GALAXY_SLOTS:-1}
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33 -o '${output_bam}'
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34 unsorted_output.bam
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35 ]]></command>
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36 <inputs>
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37 <param name="input_bam" type="data" format="bam" label="Select BAM dataset to slice" />
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38 <conditional name="slice_method">
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39 <param name="slice_method_selector" type="select" label="How do you want to slice your dataset?">
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40 <option value="bed">using a list of intervals from a BED dataset</option>
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41 <option value="chr">by chromosomes/contigs present in the BAM dataset</option>
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42 <option value="man">by chromosomes/contigs and coordinates</option>
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43 </param>
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44 <when value="bed">
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45 <param name="input_interval" type="data" format="bed" label="BED file" help="BED datasets can be obtained using &quot;Get Data -> UCSC Main&quot; datasource" />
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46 </when>
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47 <when value="chr">
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48 <param name="refs" type="select" optional="False" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Click and type in the box above to see options. You can select multiple entries. If &quot;No options available&quot; is displayed, you need to re-detect metadata on the input dataset. See help section below.">
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49
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50 <!-- The options tagset below extracts reference names from bam file metadata -->
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51 <!-- This will not work with bed files with old style metadata. However this -->
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52 <!-- Can be easily fixed by re-deceting metadata on a bam dataset by clicking -->
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53 <!-- The pencil icon and settind datatype to "bam" -->
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54 <!-- This change has been commited in the following pull request: -->
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55 <!-- https://github.com/galaxyproject/galaxy/pull/107 -->
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56
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57 <options>
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58 <filter type="data_meta" ref="input_bam" key="reference_names" />
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59 </options>
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60 </param>
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61 </when>
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62 <when value="man">
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63 <repeat name="regions" title="Regions" min="1">
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64 <param name="chrom" type="select" optional="False" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Select chromosome/contig from the list. If &quot;No options available&quot; is displayed, you need to re-detect metadata on the input dataset. See help section below.">
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65
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66 <!-- See comments above -->
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67
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68 <options>
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69 <filter type="data_meta" ref="input_bam" key="reference_names" />
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70 </options>
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71 </param>
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72 <param name="start" type="integer" min="1" value="0" label="Enter START coordinate (1-based)"/>
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73 <param name="end" type="integer" min="1" value="100" label="Enter END coordinate"/>
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74 </repeat>
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75 </when>
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76 </conditional>
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77 </inputs>
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78 <outputs>
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79 <data name="output_bam" format="bam" />
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80 </outputs>
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81 <tests>
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82 <test>
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83 <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
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84 <param name="slice_method_selector" value="bed"/>
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85 <param name="input_interval" ftype="bed" value="bam-slice.bed" />
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86 <output name="output_bam" file="bam-slice-test1.bam" ftype="bam" lines_diff="4" />
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87 </test>
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88 <test>
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89 <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
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90 <param name="slice_method_selector" value="chr"/>
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91 <param name="refs" value="chrM" />
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92 <output name="output_bam" file="bam-slice-test2.bam" ftype="bam" lines_diff="4" />
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93 </test>
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94 <test>
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95 <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
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96 <param name="slice_method_selector" value="man"/>
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97 <param name="chrom" value="chrM" />
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98 <param name="start" value="1" />
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99 <param name="end" value="1000" />
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100 <output name="output_bam" file="bam-slice-test3.bam" ftype="bam" lines_diff="4"/>
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101 </test>
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102 </tests>
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103 <help><![CDATA[
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104 **What it does**
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105
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106 Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates.
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107 BED datasets can be obtained from **Get Data -> UCSC Main**.
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108
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109 This tool is based on ``samtools view`` command.
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110
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111 @no-chrom-options@
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112 ]]></help>
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113 <expand macro="citations"/>
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114 </tool>